In Japanese Patent application Laid-Open Publication No. 2000-337182, there is shown a control device of an internal combustion engine which is provided with the above mentioned cylinder deactivation mechanism and valve operation phase variable mechanism for changing an operation phase of an intake valve. According to this control device, transient control for gradually changing from the valve operation phase for the whole cylinder operation to the valve operation phase for the partial cylinder operation is executed at the time of being shifted from the whole cylinder operation to the partial cylinder operation. According to this transient control, it is set that a transition speed of the valve operation phase decreases as a difference between an engine output torque at the time of operating the whole cylinders and the engine output torque at the time of operating the part of cylinders increases.